Judge Marina Syrova ruled Friday that the band members had "committed hooliganism driven by religious hatred." She rejected the women's arguments that they were protesting the Russian Orthodox Church's support for Putin and didn't intend to offend religious believers.
Putin himself had said the band members shouldn't be judged too harshly, creating expectations that they could be sentenced to time served and freed in the courtroom. This, however, would have left the impression that Putin had bowed to public pressure, something he has resisted throughout his 12 years in power.
Kremlin spokesman Dmitry Peskov said that Putin couldn't intervene in the judicial process and refused to comment on the sentence.
When the sentence was announced, shouts of "down with the police state" rose from a crowd of hundreds of Pussy Riot supporters outside the courtroom. More than 50 people were detained, including former world chess champion Garry Kasparov, who said police beat him.
Protesters donned the colorful balaclavas that have become a symbol of the band in many European and U.S. cities, though no single protest outside Moscow drew more than a few hundred people.
In Kiev, Ukraine, four women, one of whom was topless, used a chainsaw to cut down a cross. About 40 protesters gathered in New York held up banners that read: "We are all hooligans."
The crowd in Moscow included many of the prominent writers, journalists and opposition partisans who spearheaded the mass protests that shook the city over the winter and spring. Pussy Riot was an obscure band of activists for much of that time, and some fellow opponents of Putin disapproved of their tactics, but they rallied to the group's defense after the March arrests.
For three hours as the judge read the verdict, the defendants stood in handcuffs in a glass cage in the courtroom, the same one where oil tycoon Mikhail Khodorkovsky, another Putin opponent, was convicted two years ago.
The three women smiled sadly as the judge recounted testimony of prosecution witnesses accusing them of sacrilege and "devilish dances" in the church and said that their feminist views made them hate the Orthodox religion.
Tolokonnikova laughed out loud when the judge read the testimony of a psychologist who said that her "active stance on social issues" was an anomaly.
The three women remained calm and kept smiling after the judge announced the sentence. Someone in the courtroom shouted "Shame!" They waved at relatives from behind the glass.
The charges carried a maximum penalty of seven years in prison, though prosecutors had asked for a three-year sentence.
Popular Russian author Boris Akunin, a supporter of Pussy Riot who was outside the courthouse, said Putin "has doomed himself to another year and a half of international shame and humiliation."
"The whole thing is bad because it's yet another step toward the escalation of tensions within society. And the government is absolutely to blame," he said.
Defense lawyers said they would appeal but had little hope that the verdict would be overturned. "This verdict is the result of a political decision in the Kremlin, made by Vladimir Putin," said Mark Feygin.
He said the women would not ask for a pardon from Putin. "They will not beg and humiliate themselves before such a bastard," he said.
Another sign of the defendants' resolve came in a new song the band released Friday on the Internet: "Putin Is Lighting the Fires of Revolution."
Samutsevich's father said he had met with his daughter before the court session and she was prepared for a prison sentence. "We tried to comfort her," said Stanislav Samutsevich.
Amnesty International, which has called the women prisoners of conscience, said the court ruling "shows that the Russian authorities will stop at no end to suppress dissent and stifle civil society."
Governments including the United States, Britain, France and Germany denounced the sentences as disproportionate.
President Barack Obama was disappointed by the decision, White House spokesman Josh Earnest said. "While we understand the group's behavior was offensive to some, we have serious concerns about the way that these young women have been treated by the Russian judicial system," he said.
Further controversy was stirred up by the detention of Kasparov, now one of Putin's fiercest critics. He said he was beaten by the police who detained him, but police claimed that he bit an officer's finger. After his release, Kasparov tweeted that he was going to an emergency room "to check my injuries and to prove that I am not drunk and haven't bitten anyone."
The Pussy Riot case has helped to energize the opposition. Protest leader Alexei Navalny condemned the verdict as a "cynical mockery of justice" and said the opposition would step up its protests.
Even some Kremlin loyalists strongly criticized the verdict. Former Finance Minister Alexei Kudrin said it has dealt "yet another blow to the court system and citizens' trust in it."
"The country's image and its attractiveness in the eyes of investors have suffered an enormous damage," he said.
Mikhail Fedotov, the head of a presidential advisory council on human rights, voiced hope that the sentence will be repealed or at least softened. Mikhail Barshchevsky, a lawyer who represents the Cabinet in high courts, said that the verdict had no basis in Russian criminal law.
The Pussy Riot case has underlined the vast influence of the Russian Orthodox Church. Although church and state are formally separate, the church identifies itself as the heart of Russian national identity and critics say its strength effectively makes it a quasi-state entity. Some Orthodox groups and many believers had urged strong punishment for an action they consider blasphemous.
The head of the church, Patriarch Kirill, has made no secret of his strong support for Putin, praising his leadership as "God's miracle," and he described the punk performance as part of an assault by "enemy forces" on the church. He avoided talking to journalists Friday as he left Warsaw's Royal Castle following a ceremony in which he and the head of Poland's Catholic Church called for mutual forgiveness and reconciliation between the churches.
The Orthodox Church said in a statement after the verdict that the band's stunt was a "sacrilege" and a "reflection of rude animosity toward millions of people and their feelings." It also asked the authorities to "show clemency toward the convicted in the hope that they will refrain from new sacrilegious actions."
A handful of Orthodox activists joined the crowd outside the courthouse. "I'm glad they were punished like criminals and didn't get away with it," said Dmitry Tsorionov, holding a Bible. "They committed a grave crime and nobody should do it again."
The case comes in the wake of several recently passed laws cracking down on opposition, including one that raised the fine for taking part in an unauthorized demonstrations by 150 times to 300,000 rubles (about $9,000).
Another measure requires non-governmental organizations that both engage in vaguely defined "political activity" and receive funding from abroad to register as "foreign agents." Putin has accused foreign countries of feeding much of the dissent in Russia.
Nataliya Vasilyeva, Lynn Berry, Mansur Mirovalev and Jim Heintz contributed to this report.